#!/bin/bash
#SBATCH -t 4:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --mem=144g
#SBATCH --export=NONE
#SBATCH --mail-user=alex_labossiere@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL

rawdir=/data/mramseylab/raw_reads/2024_AL_SUPP
clsdir=/data/mramseylab/16S/classifiers/homd-classifier
visdir=/data/mramseylab/16S/visualizations/AL_2024
procdir=/data/mramseylab/16S/proc_reads/2024_AL_SUPP_6000/medias
metadata=data/mramseylab/16S/metadata/meta_BSFS.tsv

module load QIIME2/2024.2

qiime feature-classifier classify-sklearn \
  --i-classifier HOMD-classifier.qza \
  --i-reads $rawdir/pseudo-rep-seqs-v1v2-2024.qza \
  --o-classification taxonomy.qza

qiime metadata tabulate \
  --m-input-file taxonomy.qza \
  --o-visualization taxonomy.qzv